Recent Releases of swarm
swarm - swarm 3.1.5
swarm 3.1.5 fixes four minor bugs, improves code and documentation, and eliminates compilation warnings and static analysis warnings:
- change: when using the fastidious and the ceiling options, minimal ceiling value is now 40 megabytes (instead of 8 megabytes),
- add: more compilation checks (shadow, useless-cast, conversion, sign-conversion),
- add: 42 new black-box tests,
- fix: two minor bugs introduced in version 3.1.1 (alloc-dealloc-mismatch, and allocating too much memory; bugs had no impact on clustering results),
- fix: a minor bug introduced in version 3.1.4 (misaligned memory under certain conditions; bug had no impact on clustering results),
- fix: minor bug in the way available memory is estimated (buffer underflow; bug had no impact on clustering results),
- fix: 50 warnings triggered by newly added compilation checks,
- fix: 1,677 clang-tidy warnings (from 2,629 warnings, down to 952),
- performance: generally stable but compiler-dependent, with the exception of a 5 to 10% increase in total memory footprint when d >= 2 (we expect these performance regressions to be temporary and to be fixed with further refactoring),
- improve: documentation for output option --network_file (advanced users),
- improve: build target platform detection,
- improve: code-coverage of our test-suite,
- improve: code modernization for long-term maintenance,
- revert: due to inconsistent test results, reading from named pipes (fifo) is marked as experimental for now
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Published by torognes about 2 years ago
swarm - swarm 3.1.4
swarm version 3.1.4 fixes a minor bug, eliminates compilation warnings and static analysis warnings, and improves code:
- fix: add checks to prevent silent overflow of short unsigned integers,
- fix: compilation warnings with GCC 13 and clang 18,
- fix: 1,040 clang-tidy warnings (from 3,669 warnings, down to 2,629),
- improve: code modernization for long-term maintenance,
- improve: double the maximal number of threads (from 256 threads to 512),
- improve: make -DNDEBUG the default compilation behavior,
- performance: stable for all modes, except a 6 to 10% increase in memory footprint when d > 2
- C++
Published by torognes almost 3 years ago
swarm - swarm 3.1.3
Version 3.1.3 fixes a few minor bugs, removes warnings, and improves code and documentation: - fix: bug introduced in version 3.1.1, that caused swarm to allocate way too much memory when d > 1 (bug had no impact on clustering results), - fix: off-by-one error when allocating memory for a Bloom filter (bug had no impact on clustering results), - fix: compilation warning with GCC 12 (and more recent) when using link-time optimization, - fix: compilation warning with clang 13 (and more recent): unused set variable, - fix: five clang-tidy warnings (readability-braces-around-statements), - fix: minor code refactoring, - improve: more uniform vocabulary throughout swarm's documentation (code, help, manpage, README, companion scripts and wiki), - improve: code coverage of our test suite (swarm-tests).
- C++
Published by torognes over 3 years ago
swarm - swarm 3.1.2
Fix a bug with fastidious mode introduced in version 3.1.1, that could cause Swarm to crash. Probably due to allocating too much memory.
- C++
Published by torognes over 3 years ago
swarm - swarm 3.1.1
Version 3.1.1 eliminates a risk of segmentation fault with extremely long sequence headers. Documentation and error messages have been improved, and code cleaning continued.
- C++
Published by torognes over 3 years ago
swarm -
swarm 3.1.0: Improved code and documentation, bugfix, and macOS on ARM64
- C++
Published by torognes over 5 years ago
swarm - swarm 3.0.0
Version 3.0.0 introduces a faster algorithm for d = 1, and a reduced memory footprint. Swarm has been ported to Windows x86-64, GNU/Linux ARM64, and GNU/Linux POWER8. Internal code has been modernized, hardened, and thoroughly tested. Strict dereplication of input sequences is now mandatory. The --seeds option (-w) now outputs results sorted by decreasing abundance, and then by alphabetical order of sequence labels.
- C++
Published by torognes over 6 years ago
swarm - Swarm 2.2.2
Swarm 2.2.2 fixes a bug with an endless wait in rare cases with multiple threads.
- C++
Published by torognes over 8 years ago
swarm - Swarm 2.2.1
Swarm 2.2.1 fixes a memory allocation bug for d=1 that should only affect cases where the input sequences have not ben fully dereplicated.
- C++
Published by torognes over 8 years ago
swarm - Swarm 2.2.0
Version 2.2.0 fixes several problems and improves usability. Corrected output to structure and uclust files when using fastidious mode. Corrected abundance output in some cases. Added check for duplicated sequences and fixed check for duplicated sequence IDs. Checks for empty sequences. Sorts sequences by additional fields to improve stability. Improves compatibility with compilers and operating systems. Outputs sequences in upper case. Allows 64-bit abundances. Shows message when waiting for input from stdin. Improves error messages and warnings. Improves checking of command line options. Fixes remaining errors reported by test suite. Updates documentation.
- C++
Published by torognes over 8 years ago
swarm - Swarm 2.1.13
Fix bug with progress bar when writing seeds.
- C++
Published by torognes over 9 years ago
swarm - Swarm 2.1.12: Remove debugging message
Remove a debugging message
- C++
Published by torognes over 9 years ago
swarm - Swarm 2.1.11: Fix bugs with SIMD alignment when d>1
Version 2.1.11 fixes two bugs (issue #96) related to the SIMD implementation of alignment that might result in incorrect alignments and scores. The bug only applies when d>1.
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Published by torognes over 9 years ago
swarm - Swarm 2.1.10
Swarm version 2.1.10 fixes two bugs related to gap penalties of alignments. The first bug may lead to wrong alignments and similarity percentages reported in UCLUST (.uc) files. The second bug makes Swarm use a slightly higher gap extension penalty than specified. The default gap extension penalty used have actually been 4.5 instead of 4.
- C++
Published by torognes over 9 years ago
swarm - Swarm 2.1.9
Fix compilation errors with GCC version 6.
- C++
Published by torognes almost 10 years ago
swarm - SWARM 2.1.8
Fix rare bug with extremely short non-dereplicated sequences. Do not show alignment parameters for d=1.
- C++
Published by torognes over 10 years ago
swarm - SWARM 2.1.7
Fix error with seed output. Ignore CR in FASTA files. Improved help and error messsages. And more.
- C++
Published by torognes over 10 years ago
swarm - SWARM 2.1.6
Swarm 2.1.6 fixes problems with older compilers that do not have the x86intrin.h header file. It also fixes a bug in the output of seeds with the -w option when d>1.
- C++
Published by torognes over 10 years ago
swarm - SWARM 2.1.4
Swarm 2.1.4 fixes minor bugs in the algorithm used for d=1.
- C++
Published by torognes almost 11 years ago
swarm - SWARM 2.1.1
Fix a bug with the fastidious option that caused it to ignore some connections between heavy and light swarms.
- C++
Published by torognes about 11 years ago
swarm - swarm 2.1.0
Version 2.1.0 marks the first official release of swarm 2 with a number of improvements and new features: - built-in breaking phase now performed automatically - built-in strict dereplication (with d = 0) - possibility to output OTU representatives in fasta format (option -w) - fast algorithm now used by default for d = 1 (linear complexity) - a new option called fastidious that refines d = 1 results and reduces the number of small OTUs
- C++
Published by torognes over 11 years ago
swarm - QIIME-ready version 2
Release 1.2.19 brings corrections made to swarm and to the swarm_breaker.py script for a better integration with QIIME.
- C++
Published by frederic-mahe over 11 years ago
swarm - QIIME-ready version
That new release contains improvements and small modifications made to swarm and to the swarm_breaker.py script for integration into QIIME.
- C++
Published by frederic-mahe almost 12 years ago
swarm - SWARM version 1.2.6
SWARM version 1.2.6 includes an option for producing mothur-compatible output files. Also, this version will provide information about the location and kind of eventual illegal characters encountered in the input fasta file.
- C++
Published by torognes about 12 years ago
swarm - SWARM version 1.2.5
This version will run on cpus without the POPCNT feature. Just SSE2 is now required.
- C++
Published by torognes about 12 years ago
swarm - SWARM version 1.2.4
Changes the name of the new option to --break-swarms.
- C++
Published by torognes over 12 years ago
swarm - SWARM version 1.2.3
Adds the option -b or --break_swarms to output all pairs of amplicons.
- C++
Published by torognes over 12 years ago